Contacts of the strand formed by residues 115 - 120 (chain C) in PDB entry 2WZJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 4.2 10.3 - - + +
104C MET* 4.0 29.3 + - + +
105C LYS* 3.7 33.9 - - + +
113C VAL 4.1 1.2 + - - -
114C LYS* 1.3 96.1 + - - +
116C PHE* 1.3 61.1 + - - +
117C GLU 3.7 14.4 - - - +
118C VAL* 4.0 17.9 - - + -
127C LEU* 4.5 7.9 - - + -
128C VAL 3.6 21.8 - - - +
129C MET* 4.6 13.0 - - + +
351C TYR* 3.3 28.6 - - + +
359C LEU* 3.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 4.8 0.2 - - - +
78C GLU 5.5 0.9 - - - -
79C VAL* 4.0 9.9 - - + -
114C LYS* 4.1 9.9 - - + -
115C LEU* 1.3 78.0 - - - +
117C GLU* 1.3 58.1 + - - +
128C VAL* 2.8 19.3 + - + +
129C MET 3.8 18.2 - - - -
130C GLU* 3.6 44.2 - - + -
351C TYR* 3.6 16.5 - - - -
355C MET* 4.5 0.7 - - - +
356C ALA* 3.3 31.5 + - + +
359C LEU* 3.8 27.5 - - + +
360C LEU* 3.5 31.6 - - + -
363C TYR* 3.7 31.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLY* 5.8 0.5 - - - -
52C ASN* 5.6 2.8 + - - +
53C TYR* 2.5 47.9 + - - +
72C HIS* 5.1 1.7 + - - -
115C LEU* 3.7 3.1 - - - +
116C PHE* 1.3 81.5 - - - +
118C VAL* 1.3 71.7 + - - +
119C ILE* 3.8 22.3 - - + +
128C VAL* 3.0 33.1 + - + +
351C TYR* 3.6 16.1 - - - +
352C ASN* 3.8 6.0 - - - +
353C GLU* 3.3 34.5 + - - +
356C ALA* 3.5 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 6.3 1.3 - - + -
101C VAL* 4.2 13.0 - - + -
105C LYS* 4.5 12.1 - - - +
115C LEU* 4.0 20.9 - - + -
117C GLU* 1.3 77.1 - - - +
119C ILE* 1.3 65.0 + - - +
120C GLU* 4.3 4.8 + - + +
125C LEU* 3.7 26.0 - - + -
126C TYR 3.6 3.4 - - - -
127C LEU* 3.6 22.7 - - + -
351C TYR* 3.1 21.2 + - + +
352C ASN* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.5 18.4 - - + -
51C GLY* 4.3 16.2 - - - +
53C TYR* 4.2 23.8 - - + -
117C GLU* 3.8 25.8 - - + +
118C VAL* 1.3 75.7 - - - +
120C GLU* 1.3 65.7 + - - +
121C THR* 4.3 4.7 - - + +
125C LEU* 3.4 5.0 - - - +
126C TYR* 2.8 55.8 + - + +
128C VAL* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS* 3.3 27.3 + - - +
98C PHE* 3.4 33.4 - - - -
118C VAL* 4.2 5.0 + - + +
119C ILE* 1.3 77.4 - - - +
121C THR* 1.3 67.4 + - - +
124C THR 3.6 4.0 - - - +
125C LEU* 3.7 14.3 - - + +
168D GLN 4.7 6.0 - - - +
170D PHE* 3.9 7.8 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il